Conventional methods for biomolecule detection such as DNA sequencing include use of optical detection technologies. Among existing optical methods, an array of wells is used to immobilize polymerase molecules and to act as zero mode waveguides such that only the fluorescence near the surface and at the polymerase is detected. Although incorporation of a modified nucleotide is observed via fluorescent tags, problems arise. The problems are associated with the capture and fluorescence efficiency of the single molecule signal. Namely the laser used in the fluorophore excitation heats the enzymes, reducing the read length in each well and ultimately compromising the accuracy of the system. In addition, enzymes immobilized in the wells become inactive and the sequences in these wells cannot be read.
In general, important parameters for evaluating a sequencing technique include accuracy, cost, throughput, time to result, and system size. For example, the tolerable level of error is accepted to be 1 in 10,000 bases sequenced. With this level of accuracy, existing systems are bulky with high cost and take long time to sequence a human genome. For example, large optical detection systems are used for human genome sequencing (3 billion base pairs) with sizes comparable to a refrigerator and the cost is about $30K in reagents (excluding the overhead cost of the sequencer) with about a week or longer to complete. In another example for CMOS-based sequencing methods, over 1000 chips were used with a reported cost exceeding $2 million to extract the full genome of Gordon Moore.
There is a need for providing devices, methods, and systems for portable, accurate, cost effective, easy-to-use, and high throughput biochemical detections.